Pharmaceutical proteins comprise a large and rapidly growing segment of the pharmaceutical market. To be safe and effective, pharmaceutical proteins must possess not only the correct covalent structure, but also the correct non-covalent three-dimensional folded structure - and there is no existing method capable of guaranteeing this conformational integrity on a quality assurance (QA) basis. A technology known as hydroxyl radical protein footprinting (HRFP) has been described for the rigorous structural comparison of recombinant pharmaceutical proteins with FDA-approved formulations. HRFP uses a burst of short-lived hydroxyl (OH.) radicals to react with amino acids on the protein surface, creating modifications easily recognized by liquid chromatography coupled to mass spectrometry (LCMS). For QA, results of HRFP from a test sample of a protein must match HRFP results from the protein standard. Otherwise, the structure of the test sample has been compromised. In cases where differences between standard and sample are observed, the general location of these abnormalities can be determined, aiding in troubleshooting. While the method exhibits strong potential as an analytical and QA tool, HRFP requires a substantial degree of highly specialized expertise to generate data sufficiently reliable for use as a QA method. We propose an automated platform for executing the entire HRFP process. Practically, and philosophically, the platform will be inserted into the existing automated workflow of bottom-up protein analysis by mass spectrometry. We propose to produce an automated sample handling and flash photolysis system, alternate schemes for flash photolytic generation of hydroxyl radicals, QA monitors for each step of HRFP, and statistical quality assurance computer programs. We will demonstrate the ability of the integrated system to detect structural abnormalities with current pharmaceutical proteins. The resulting system will be a single-vendor automated HRFP platform for insertion into already-existing LCMS systems allowing application of this technology by researchers with a conventional level of expertise in protein mass spectrometry.